Difference between revisions of "4DUSandEndoscope"

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Jan Gumprecht
 
Jan Gumprecht
 
* E-Mail: jgumprec(at)bwh.harvard.edu
 
* E-Mail: jgumprec(at)bwh.harvard.edu
 +
* Location: Kyushu, Japan
 +
* Timezone: GMT + 9
  
 
Jae-Sung Hung, PhD
 
Jae-Sung Hung, PhD
 
* E-Mail: hong(at)dem.med.kyushu-u.ac.jp
 
* E-Mail: hong(at)dem.med.kyushu-u.ac.jp
 +
* Location: Kyushu, Japan
 +
* Timezone: GMT + 9
  
 
Nobuhiko Hata, PhD
 
Nobuhiko Hata, PhD
 
* E-Mail: hata(at)bwh.harvard.edu
 
* E-Mail: hata(at)bwh.harvard.edu
 +
* Location: Boston, USA
 +
* Timezone: GMT - 5
  
 
Haiying Liu
 
Haiying Liu
 
* E-Mail: hliu(at)bwh.harvard.edu
 
* E-Mail: hliu(at)bwh.harvard.edu
 +
* Location: Boston, USA
 +
* Timezone: GMT - 5
  
 
Yamada Atsushi, PhD
 
Yamada Atsushi, PhD
 
* E-Mail: yamada.atsushi(at)nitech.ac.jp
 
* E-Mail: yamada.atsushi(at)nitech.ac.jp
 +
* Location: Nagoya, Japan
 +
* Timezone: GMT + 9
 +
 +
== Project Description ==
 +
 +
The goal of this project is to create a new 3D Slicer Module that can overlay patient registered 4D US volumes with endoscopic images.
 +
 +
The Project is divided into four part: 4D Ultrasound Volume Reconstruction, Patient-Image Registration, Endoscope Overlay, and Endoscope Calibration. All four parts will be accessable through a single 3D Slicer Module.
 +
 +
[[Image:ModuleWorkflow.png | 600px ]]
 +
 +
=== Overall Progress ===
 +
 +
{| border="0" cellpadding="3" cellspacing=0
 +
 +
|- bgcolor="#abcdef"
 +
 +
! Month !! Week #  !! Start Date - End Date !! Done !! Date Done
 +
 +
|-
 +
 +
|height=5|
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 34 !! 17.08 - 23.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 33 !! 10.08 - 16.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| || colspan="2" |  Endoscopic Overlay and Endoscopic Calibration shall be finished  ||align="center" |  ||
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
!| August !! Week 32 !! 03.08.09 - 09.08.09 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
|-
 +
 +
| || colspan="2" | New PC set up ||align="center" | x || Thu Jul, 30th
 +
 +
|-
 +
 +
| || colspan="2" | New PC arrived ||align="center" | x || Tue Jul, 28th
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 31 !! 27.07 - 02.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| width="80" | || colspan="2" width="550" | Project Page created  ||align="center" width="50" | x || width="120" | Fri Jul, 24th
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
 +
 +
|-
 +
 +
|}
 +
 +
=== General To Do ===
 +
 +
{|border="0" cellpadding="5"
 +
 +
|- bgcolor="silver"
 +
 +
! colspan="2" | Tasks
 +
 +
|-
 +
 +
| align="center" width="70px" | O || align="left" width="730px"|Fill Project Page with Information
 +
 +
|-
 +
 +
| align="center" width="70px" | O || align="left" width="730px"|Order new Frame Grabber Card
 +
 +
|-
 +
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" width="730px"|Set Up New Computer
 +
 +
|-
 +
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" width="730px"|Order new PC
 +
 +
|-
 +
 +
| align="center" bgcolor="#009900" | DONE || align="left" | Create Project Page
 +
 +
|-
 +
 +
|}
 +
 +
=== Details ===
 +
 +
* The following frame grabber card only provides grayscale images: I-O DATA GV-VCP3R/PCI (video decoder chip CX2388x) [http://www.iodata.jp/product/tv/capture/gv-vcp3pci/index.htm]
 +
 +
 +
----
 +
----
 +
 +
== 3D Slicer Module ==
 +
 +
 +
 +
* Responsible: Jan Gumprecht
 +
=== Details ===
 +
* The module is available through svn: http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/4DUsEndoNav/
 +
 +
=== Progress ===
 +
 +
{| border="0" cellpadding="3" cellspacing=0
 +
 +
|- bgcolor="#abcdef"
 +
 +
! Month !! Week #  !! Start Date - End Date !! Done !! Date Done
 +
 +
|-
 +
 +
|height=5|
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 34 !! 17.08 - 23.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 33 !! 10.08 - 16.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| width="80px"| || colspan="2" width="550px"| Source Code checked in to svn ||align="center" width="50px" |  x || width="120px" |  Thu, Aug 6th
 +
 +
|-
 +
 +
| width="80px"| || colspan="2" width="550px"| Second Window works ||align="center" width="50px" |  x || width="120px" |  Thu, Aug 6th
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
!| August !! Week 32 !! 03.08.09 - 09.08.09 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| width="80px"| || colspan="2" width="550px"| Created First prototype of module ||align="center" width="50px" |  x || width="120px" |  Fri, Jul 31st
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 31 !! 27.07 - 02.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
 +
 +
|-
 +
 +
|}
 +
 +
=== To Do ===
 +
 +
{|border="0" cellpadding="5"
 +
 +
|- bgcolor="silver"
 +
 +
! colspan="2" | Tasks
 +
 +
|-
 +
 +
| align="center" width="70px" | O || align="left" | Close Second window with OS native commands, i.e. click the "X" in the right upper corner
 +
 +
|-
 +
 +
| align="center" width="70px" | O || align="left" | Comprehend Prostate nav module's source code
 +
 +
|-
 +
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" | Check in source to svn
 +
 +
|-
 +
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" | Include Second Window source code
 +
 +
|-
 +
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left"| Create first prototyp of module, i.e. adapt IGTWizard Module
 +
 +
|-
 +
 +
|}
 +
 +
 +
----
 +
 +
----
 +
 +
== 4D Ultrasound Volume Reconstruction==
 +
* Responsible: Jan Gumprecht
 +
=== Details ===
 +
 +
The project is described here: [[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht]]
 +
 +
=== Progress ===
 +
 +
{| border="0" cellpadding="3" cellspacing=0
 +
 +
|- bgcolor="#abcdef"
 +
 +
! Month !! Week #  !! Start Date - End Date !! Done !! Date Done
 +
 +
|-
 +
 +
|height=5|
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 34 !! 17.08 - 23.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 33 !! 10.08 - 16.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
!| August !! Week 32 !! 03.08.09 - 09.08.09 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" | Update Calibration and Spacing Handeling  || width="50" align="center" |  || width="120" |
 +
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" | New Commandline parameter added to grab a test image  || width="50" align="center" | x || width="120" | Tue, Jul 30th
 +
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" | All parameters of the calibration file are now used  || width="50" align="center" | x || width="120" | Tue, Jul 28th
 +
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" | OpenIGTLink is now externally, no local copy within the source code is used anymore  || width="50" align="center" | x || width="120" | Mon, Jul 27th
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 31 !! 27.07 - 02.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" | Show demo of the system  || width="50" align="center" |  || width="120" |
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
 +
 +
|-
 +
 +
|}
 +
 +
=== To Do ===
 +
 +
{|border="0" cellpadding="5"
 +
 +
|- bgcolor="silver"
 +
 +
! colspan="2" | Tasks
 +
 +
|-
 +
 +
| align="center" width="70px" s| O || align="left" width="730"| Find Segmentation Fault
 +
 +
|-
 +
 +
| align="center" width="70px" | O || align="left" width="730"| Update Handling of Spacing
 +
 +
|-
 +
 +
| align="center" width="70px" | O || align="left" width="730"| Update Calibration Part
 +
 +
|-
 +
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" width="730"| Set up existing Hardware for first demo
 +
 +
|-
 +
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" width="730"| Update CalibrationFileReader
 +
 +
|-
 +
 +
|}
 +
 +
 +
 +
----
 +
 +
----
 +
 +
== Patient-Image Registration ==
 +
* Responsible: Jae-Sung Hong
 +
 +
=== Details ===
 +
 +
=== Progress ===
 +
 +
{| border="0" cellpadding="3" cellspacing=0
 +
 +
|- bgcolor="#abcdef"
 +
 +
! Month !! Week #  !! Start Date - End Date !! Done !! Date Done
 +
 +
|-
 +
 +
|height=5|
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 34 !! 17.08 - 23.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 33 !! 10.08 - 16.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
!| August !! Week 32 !! 03.08.09 - 09.08.09 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| width="80"| || colspan="2" width="550"| Start integration with 4D Ultrasound ||align="center" width="50" |  || width="120" |
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 31 !! 27.07 - 02.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
 +
 +
|-
 +
 +
|}
 +
 +
=== To Do ===
 +
 +
{|border="0" cellpadding="5"
 +
 +
|- bgcolor="silver"
 +
 +
! colspan="2" | Tasks
 +
 +
|-
 +
 +
| align="center" width="70px" | O || align="left" width="730"|Dummy Task
 +
 +
|-
 +
 +
|}
 +
 +
 +
 +
----
 +
 +
----
 +
 +
== Endoscope Overlay ==
 +
* Responsible: Yamada Atsushi, Haiying Liu
 +
=== Details ===
 +
* [http://www.na-mic.org/Wiki/index.php/OpenCV_Module_in_Slicer3 OpenCV Module in Slicer3]
 +
* [http://www.na-mic.org/Wiki/index.php/Slicer3_FlexibleLayouts Multiple Camera Support in Slicer3]
 +
* [http://wiki.ncigt.org/index.php/U41:Prostate:BRP:Common_Module_For_Multiple_Robots Transrectal/Transperineal biopsy robot module merge]
 +
* [http://opencv.willowgarage.com/wiki/ Open CV Wiki]
 +
* [http://wiki.intelli-si.org/index.php?title=2009SummerSecondDisplayProject Summer Second Display Project] (Japanese)
 +
 +
=== Bug Fixes for the 3D Slicer Module ===
 +
 +
* There is a bug in OpenCV related to V4L2 devices:
 +
** Here is the bugtrac with information: [[https://bugs.launchpad.net/ubuntu/+source/linux/+bug/260251]]
 +
*** Somehow this is related to bttv 878 cards. OpenCV seem not to be able to handle all output of the card correctly
 +
** Here is the fix [[http://opencvlibrary.svn.sourceforge.net/viewvc/opencvlibrary/trunk/opencv/src/highgui/cvcap_v4l.cpp?r1=1604&r2=1609]]
 +
*** Apply the changes of revision 1609 to the file # opencv/src/highgui/cvcap_v4l.cpp
 +
 +
=== Progress ===
 +
 +
{| border="0" cellpadding="3" cellspacing=0
 +
 +
|- bgcolor="#abcdef"
 +
 +
! Month !! Week #  !! Start Date - End Date !! Done !! Date Done
 +
 +
|-
 +
 +
|height=5|
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 34 !! 17.08 - 23.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 33 !! 10.08 - 16.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" |  Endoscopic Overlay shall be finished  ||align="center" width="50" |  || width="120" |
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
!| August !! Week 32 !! 03.08.09 - 09.08.09 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| || colspan="2" |  ||align="center" |  ||
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 31 !! 27.07 - 02.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
 +
 +
|-
 +
 +
|}
 +
 +
=== To Do ===
 +
 +
{|border="0" cellpadding="5"
 +
 +
|- bgcolor="silver"
 +
 +
! colspan="2" | Tasks
 +
 +
|-
 +
 +
| align="center" width="70px" | O || align="left" width="730"|Dummy Task
 +
 +
|- bgcolor="silver"
 +
 +
! colspan="2" | Endoscope overlay
 +
|-
 +
 +
|}
 +
 +
 +
 +
----
 +
 +
----
 +
 +
== Endoscope Calibration ==
 +
* Responsible: Dr. Yang
 +
=== Details ===
 +
 +
=== Progress ===
 +
 +
{| border="0" cellpadding="3" cellspacing=0
 +
 +
|- bgcolor="#abcdef"
 +
 +
! Month !! Week #  !! Start Date - End Date !! Done !! Date Done
 +
 +
|-
 +
 +
|height=5|
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 34 !! 17.08 - 23.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 33 !! 10.08 - 16.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" |  Endoscopic Calibration shall be finished  ||align="center" width="50"|  || width="120" |
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
!| August !! Week 32 !! 03.08.09 - 09.08.09 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|-
 +
 +
| || colspan="2" |  ||align="center" |  ||
 +
 +
|- bgcolor="#E8E8E8"
 +
 +
!bgcolor="#FFFFFF"| !! Week 31 !! 27.07 - 02.08 || ||
 +
 +
|-
 +
 +
|height="10px" |
 +
 +
|- bgcolor="#D0D0D0"
 +
 +
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
 +
 +
|-
 +
 +
|}
 +
 +
=== To Do ===
 +
 +
{|border="0" cellpadding="5"
 +
 +
|- bgcolor="silver"
 +
 +
! colspan="2" | Tasks
 +
 +
|-
 +
 +
| align="center" width="70px" | O || align="left" width="730"| Dummy Task
 +
 +
|-
 +
 +
|}

Latest revision as of 05:23, 11 April 2023

Home < 4DUSandEndoscope

Project Page for 4D Ultrasound with Endoscopic Overlay

Collaborators

Jan Gumprecht

  • E-Mail: jgumprec(at)bwh.harvard.edu
  • Location: Kyushu, Japan
  • Timezone: GMT + 9

Jae-Sung Hung, PhD

  • E-Mail: hong(at)dem.med.kyushu-u.ac.jp
  • Location: Kyushu, Japan
  • Timezone: GMT + 9

Nobuhiko Hata, PhD

  • E-Mail: hata(at)bwh.harvard.edu
  • Location: Boston, USA
  • Timezone: GMT - 5

Haiying Liu

  • E-Mail: hliu(at)bwh.harvard.edu
  • Location: Boston, USA
  • Timezone: GMT - 5

Yamada Atsushi, PhD

  • E-Mail: yamada.atsushi(at)nitech.ac.jp
  • Location: Nagoya, Japan
  • Timezone: GMT + 9

Project Description

The goal of this project is to create a new 3D Slicer Module that can overlay patient registered 4D US volumes with endoscopic images.

The Project is divided into four part: 4D Ultrasound Volume Reconstruction, Patient-Image Registration, Endoscope Overlay, and Endoscope Calibration. All four parts will be accessable through a single 3D Slicer Module.

ModuleWorkflow.png

Overall Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
Endoscopic Overlay and Endoscopic Calibration shall be finished
August Week 32 03.08.09 - 09.08.09
New PC set up x Thu Jul, 30th
New PC arrived x Tue Jul, 28th
Week 31 27.07 - 02.08
Project Page created x Fri Jul, 24th
July Week 30 20.07.09 - 26.07.09

General To Do

Tasks
O Fill Project Page with Information
O Order new Frame Grabber Card
DONE Set Up New Computer
DONE Order new PC
DONE Create Project Page

Details

  • The following frame grabber card only provides grayscale images: I-O DATA GV-VCP3R/PCI (video decoder chip CX2388x) [1]


3D Slicer Module

  • Responsible: Jan Gumprecht

Details

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
Source Code checked in to svn x Thu, Aug 6th
Second Window works x Thu, Aug 6th
August Week 32 03.08.09 - 09.08.09
Created First prototype of module x Fri, Jul 31st
Week 31 27.07 - 02.08
July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Close Second window with OS native commands, i.e. click the "X" in the right upper corner
O Comprehend Prostate nav module's source code
DONE Check in source to svn
DONE Include Second Window source code
DONE Create first prototyp of module, i.e. adapt IGTWizard Module


4D Ultrasound Volume Reconstruction

  • Responsible: Jan Gumprecht

Details

The project is described here: [[2]]

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
August Week 32 03.08.09 - 09.08.09
Update Calibration and Spacing Handeling
New Commandline parameter added to grab a test image x Tue, Jul 30th
All parameters of the calibration file are now used x Tue, Jul 28th
OpenIGTLink is now externally, no local copy within the source code is used anymore x Mon, Jul 27th
Week 31 27.07 - 02.08
Show demo of the system
July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Find Segmentation Fault
O Update Handling of Spacing
O Update Calibration Part
DONE Set up existing Hardware for first demo
DONE Update CalibrationFileReader


Patient-Image Registration

  • Responsible: Jae-Sung Hong

Details

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
August Week 32 03.08.09 - 09.08.09
Start integration with 4D Ultrasound
Week 31 27.07 - 02.08


July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Dummy Task


Endoscope Overlay

  • Responsible: Yamada Atsushi, Haiying Liu

Details

Bug Fixes for the 3D Slicer Module

  • There is a bug in OpenCV related to V4L2 devices:
    • Here is the bugtrac with information: [[3]]
      • Somehow this is related to bttv 878 cards. OpenCV seem not to be able to handle all output of the card correctly
    • Here is the fix [[4]]
      • Apply the changes of revision 1609 to the file # opencv/src/highgui/cvcap_v4l.cpp

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
Endoscopic Overlay shall be finished
August Week 32 03.08.09 - 09.08.09
Week 31 27.07 - 02.08
July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Dummy Task
Endoscope overlay


Endoscope Calibration

  • Responsible: Dr. Yang

Details

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
Endoscopic Calibration shall be finished
August Week 32 03.08.09 - 09.08.09
Week 31 27.07 - 02.08
July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Dummy Task
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